Hello, mattcol18,
Let me help share information about the pay now button feature.
QuickBooks integrate with hundreds of third-party software developers.
When it comes to integrating and processing transactions, it would be best to contact the third-party application provider since the transactions that sync and created into your QuickBooks Online account depends from the third party app on how it works.They can guide and walk you through on how to handle transactions.
To give you additional information about the pay now button feature, you can read this article: Create an invoice your customer can pay online.
For future reference, you might find this article helpful: How to record a customer payment.
If there’s anything else you need help with in managing your transactions, feel free to reach back out. Have a great day!
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